Question: PICARD AlignmentSummaryMetrics for RNA-Seq
0
gravatar for rachanaj
3.4 years ago by
rachanaj0
rachanaj0 wrote:

Hi

I used the following command to gather summary metrics for my bam file generated via bowtie2 (tophat to be specific):

java -jar /usr/share/picard-tools-1.136/picard.jar CollectAlignmentSummaryMetrics INPUT=Sample_DY10.tophat.bam OUTPUT=tmpmetrics/alignmentmetrics R=/mnt/storage/ref_genome/Homo_sapiens/UCSC_hg19/UCSC/hg19/Sequence/Bowtie2Index/genome.fa

The output file is here: https://drive.google.com/file/d/0B2tk2ztVP7NIa1NNM2FrMi1WSjg/view?usp=sharing

The question I have is that the metrics PF_HQ_MEDIAN_MISMATCHES has a very high number (66). When I look at NM tag in the bam file, I see that the median is 1 with max NM = 2 I am wondering how this number is calculated by PICARD.

Any help is appreciated.

ADD COMMENTlink modified 3.3 years ago • written 3.4 years ago by rachanaj0
0
gravatar for rachanaj
3.3 years ago by
rachanaj0
rachanaj0 wrote:

This was answered on GATK forum. See here: http://gatkforums.broadinstitute.org/gatk/discussion/8353/picard-alignmentsummarymetrics#latest

ADD COMMENTlink written 3.3 years ago by rachanaj0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2041 users visited in the last hour